Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
bam{:bash}
:file
A sorted (with samtools sort) and trimmed (with iVar trim) bam file
*.bam
fasta{:bash}
:file
The reference sequence used for mapping and generating the BAM file
*.fa
fai{:bash}
:file
The index for the reference sequence used for mapping and generating the BAM file
*.fai
gff{:bash}
:file
A GFF file in the GFF3 format can be supplied to specify coordinates of open reading frames (ORFs). In absence of GFF file, amino acid translation will not be done.
*.gff
save_mpileup{:bash}
:boolean
Save mpileup file generated by ivar variants
*.mpileup
Output
name:type
description
pattern
tsv{:bash}
meta{:bash}
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*.tsv{:bash}
:file
iVar generated TSV file with the variants
*.tsv
mpileup{:bash}
meta{:bash}
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*.mpileup{:bash}
:file
mpileup output from samtools mpileup [OPTIONAL]
*.mpileup
versions{:bash}
versions.yml{:bash}
:file
File containing software versions
versions.yml
Tools
ivar
GPL-3.0-or-later
iVar - a computational package that contains functions broadly useful for viral amplicon-based sequencing.
